Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle

Detalhes bibliográficos
Autor(a) principal: Bernardes, Priscila Arrigucci [UNESP]
Data de Publicação: 2019
Outros Autores: Nascimento, Guilherme Batista do, Savegnago, Rodrigo Pelicioni, Buzanskas, Marcos Eli, Watanabe, Rafael Nakamura [UNESP], Almeida Regitano, Luciana Correia de, Coutinho, Luiz Lehmann, Gondro, Cedric, Munari, Danisio Prado [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1038/s41598-019-54382-w
http://hdl.handle.net/11449/197564
Resumo: This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.
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spelling Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattleThis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, Sao Paulo, SP, BrazilCtr Univ Adamantina, Sao Paulo, SP, BrazilInst Zootecnia, Sao Paulo, SP, BrazilUniv Fed Paraiba, Ctr Ciencias Agr, Areia, PB, BrazilEmbrapa Pecuaria Sudeste, Sao Paulo, SP, BrazilUniv Sao Paulo, Dept Zootecnia, Escola Super Agr Luiz de Queiroz, Sao Paulo, SP, BrazilMichigan State Univ, Dept Anim Sci, Coll Agr & Nat Resources, E Lansing, MI 48824 USAUniv Estadual Paulista, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, Sao Paulo, SP, BrazilFAPESP: 2015/25096-6FAPESP: 2016/22940-3FAPESP: 2013/20091-0FAPESP: 2013/19335-2FAPESP: 2012/23638-8Nature Publishing GroupUniversidade Estadual Paulista (Unesp)Ctr Univ AdamantinaInst ZootecniaUniv Fed ParaibaEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade de São Paulo (USP)Michigan State UnivBernardes, Priscila Arrigucci [UNESP]Nascimento, Guilherme Batista doSavegnago, Rodrigo PelicioniBuzanskas, Marcos EliWatanabe, Rafael Nakamura [UNESP]Almeida Regitano, Luciana Correia deCoutinho, Luiz LehmannGondro, CedricMunari, Danisio Prado [UNESP]2020-12-11T03:46:41Z2020-12-11T03:46:41Z2019-11-29info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article10http://dx.doi.org/10.1038/s41598-019-54382-wScientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019.2045-2322http://hdl.handle.net/11449/19756410.1038/s41598-019-54382-wWOS:000499892600001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengScientific Reportsinfo:eu-repo/semantics/openAccess2024-06-06T13:42:21Zoai:repositorio.unesp.br:11449/197564Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:55:56.123867Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
title Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
spellingShingle Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
Bernardes, Priscila Arrigucci [UNESP]
title_short Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
title_full Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
title_fullStr Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
title_full_unstemmed Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
title_sort Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
author Bernardes, Priscila Arrigucci [UNESP]
author_facet Bernardes, Priscila Arrigucci [UNESP]
Nascimento, Guilherme Batista do
Savegnago, Rodrigo Pelicioni
Buzanskas, Marcos Eli
Watanabe, Rafael Nakamura [UNESP]
Almeida Regitano, Luciana Correia de
Coutinho, Luiz Lehmann
Gondro, Cedric
Munari, Danisio Prado [UNESP]
author_role author
author2 Nascimento, Guilherme Batista do
Savegnago, Rodrigo Pelicioni
Buzanskas, Marcos Eli
Watanabe, Rafael Nakamura [UNESP]
Almeida Regitano, Luciana Correia de
Coutinho, Luiz Lehmann
Gondro, Cedric
Munari, Danisio Prado [UNESP]
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Ctr Univ Adamantina
Inst Zootecnia
Univ Fed Paraiba
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
Universidade de São Paulo (USP)
Michigan State Univ
dc.contributor.author.fl_str_mv Bernardes, Priscila Arrigucci [UNESP]
Nascimento, Guilherme Batista do
Savegnago, Rodrigo Pelicioni
Buzanskas, Marcos Eli
Watanabe, Rafael Nakamura [UNESP]
Almeida Regitano, Luciana Correia de
Coutinho, Luiz Lehmann
Gondro, Cedric
Munari, Danisio Prado [UNESP]
description This study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.
publishDate 2019
dc.date.none.fl_str_mv 2019-11-29
2020-12-11T03:46:41Z
2020-12-11T03:46:41Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1038/s41598-019-54382-w
Scientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019.
2045-2322
http://hdl.handle.net/11449/197564
10.1038/s41598-019-54382-w
WOS:000499892600001
url http://dx.doi.org/10.1038/s41598-019-54382-w
http://hdl.handle.net/11449/197564
identifier_str_mv Scientific Reports. London: Nature Publishing Group, v. 9, 10 p., 2019.
2045-2322
10.1038/s41598-019-54382-w
WOS:000499892600001
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Scientific Reports
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 10
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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